5KDT

Structure of the human GluN1/GluN2A LBD in complex with GNE0723

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d5kdtb_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	Phosphate binding protein-like	N-methyl-D-aspartate receptor subunit 1	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5kdta_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like II	Periplasmic binding protein-like II	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ], Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	SBP_bac_3_1st	e5kdtB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_3_1st	ECOD (1.6)
B	Lig_chan_1	e5kdtB2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: Lig_chan_1	ECOD (1.6)
A	SBP_bac_3_1st	e5kdtA2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_3_1st	ECOD (1.6)
A	Lig_chan_5	e5kdtA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: Lig_chan_5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family
B	PF10613	Ligated ion channel L-glutamate- and glycine-binding site (Lig_chan-Glu_bd)	Ligated ion channel L-glutamate- and glycine-binding site	This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine [2]. It is found in association with Lig_chan, Pfam:PF ...	This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine [2]. It is found in association with Lig_chan, Pfam:PF00060.	Domain
A	PF00060	Ligand-gated ion channel (Lig_chan)	Ligand-gated ion channel	-	Family
A	PF10613	Ligated ion channel L-glutamate- and glycine-binding site (Lig_chan-Glu_bd)	Ligated ion channel L-glutamate- and glycine-binding site	This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine [2]. It is found in association with Lig_chan, Pfam:PF ...	This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine [2]. It is found in association with Lig_chan, Pfam:PF00060.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Glutamate receptor ionotropic, NMDA 1	transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity glutamate receptor activity gated channel activity signaling receptor activity carboxylic acid transmembrane transporter activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transmitter-gated channel activity organic acid transmembrane transporter activity transmembrane transporter activity organic anion transmembrane transporter activity amide binding amyloid-beta binding binding peptide binding cation binding organic acid binding ion binding anion binding glycine binding amino acid binding carboxylic acid binding small molecule binding protein-containing complex binding protein binding calmodulin binding calcium ion binding metal ion binding monoatomic cation transmembrane transporter activity ligand-gated calcium channel activity ligand-gated monoatomic cation channel activity calcium channel activity glutamate-gated calcium ion channel activity monoatomic cation channel activity calcium ion transmembrane transporter activity metal ion transmembrane transporter activity glutamate binding	developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular response to stimulus positive regulation of cell communication regulation of postsynaptic membrane potential system process developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular response to stimulus positive regulation of cell communication regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality positive regulation of cellular process trans-synaptic signaling regulation of biological process regulation of signaling cell surface receptor signaling pathway nervous system process biological regulation cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication cellular process excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling regulation of neuronal synaptic plasticity regulation of synaptic plasticity inorganic ion homeostasis chemical homeostasis homeostatic process monoatomic ion homeostasis calcium ion homeostasis monoatomic cation homeostasis regulation of localization regulation of calcium ion transport positive regulation of cation transmembrane transport positive regulation of calcium ion transport cellular localization regulation of calcium ion transport into cytosol transport monoatomic ion transmembrane transport regulation of monoatomic ion transmembrane transport calcium ion transport metal ion transport monoatomic cation transmembrane transport regulation of calcium ion transmembrane transport localization positive regulation of monoatomic ion transport positive regulation of calcium ion transmembrane transport positive regulation of transmembrane transport monoatomic ion transport positive regulation of monoatomic ion transmembrane transport monoatomic cation transport regulation of metal ion transport calcium ion transmembrane import into cytosol regulation of transport regulation of monoatomic ion transport positive regulation of cytosolic calcium ion concentration inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport positive regulation of calcium ion transport into cytosol regulation of transmembrane transport positive regulation of transport regulation of cellular localization regulation of monoatomic cation transmembrane transport calcium ion transmembrane transport calcium ion transport into cytosol positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process protein-containing complex organization protein heterotetramerization cellular component organization cellular component biogenesis cellular component assembly protein complex oligomerization protein tetramerization protein-containing complex assembly cellular component organization or biogenesis protein heterooligomerization synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission positive regulation of synaptic transmission, glutamatergic response to acid chemical response to glycine response to chemical response to oxygen-containing compound response to nitrogen compound response to amino acid response to light stimulus learning learning or memory visual learning visual behavior cognition associative learning behavior response to radiation response to abiotic stimulus alkene metabolic process cellular response to xenobiotic stimulus propylene metabolic process hydrocarbon metabolic process xenobiotic metabolic process response to xenobiotic stimulus cellular response to chemical stimulus olefinic compound metabolic process olefin metabolic process response to alcohol response to ethanol ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway glutamate receptor signaling pathway reactive oxygen species biosynthetic process positive regulation of reactive oxygen species biosynthetic process reactive oxygen species metabolic process regulation of reactive oxygen species biosynthetic process positive regulation of reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process excitatory chemical synaptic transmission	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane synaptic cleft extracellular region somatodendritic compartment cell projection cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane synaptic cleft extracellular region somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection intracellular anatomical structure cytoplasm neuron spine dendritic spine membrane-bounded organelle transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle presynapse cytoplasmic vesicle synaptic vesicle organelle secretory vesicle vesicle exocytic vesicle axon axon terminus distal axon terminal bouton neuron projection terminus protein-containing complex plasma membrane protein complex membrane protein complex transporter complex NMDA selective glutamate receptor complex receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex cell surface organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane excitatory synapse postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse
A	Glutamate receptor ionotropic, NMDA 2A	transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity transmitter-gated monoatomic ion channel activity molecular transducer activity monoatomic ion channel activity voltage-gated channel activity voltage-gated monoatomic ion channel activity glutamate-gated receptor activity neurotransmitter receptor activity ligand-gated channel activity passive transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity transmembrane signaling receptor activity transporter activity NMDA glutamate receptor activity glutamate receptor activity gated channel activity signaling receptor activity carboxylic acid transmembrane transporter activity ligand-gated monoatomic ion channel activity extracellular ligand-gated monoatomic ion channel activity amino acid transmembrane transporter activity channel activity monoatomic ion transmembrane transporter activity transmitter-gated channel activity organic acid transmembrane transporter activity transmembrane transporter activity organic anion transmembrane transporter activity amide binding amyloid-beta binding binding peptide binding monoatomic cation transmembrane transporter activity ligand-gated calcium channel activity ligand-gated monoatomic cation channel activity calcium channel activity glutamate-gated calcium ion channel activity monoatomic cation channel activity calcium ion transmembrane transporter activity metal ion transmembrane transporter activity transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential postsynaptic neurotransmitter receptor activity neurotransmitter receptor activity involved in regulation of postsynaptic membrane potential cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	response to stimulus response to chemical response to xenobiotic stimulus developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular response to stimulus response to stimulus response to chemical response to xenobiotic stimulus developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cellular response to stimulus positive regulation of cell communication regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality positive regulation of cellular process trans-synaptic signaling regulation of biological process regulation of signaling cell surface receptor signaling pathway nervous system process biological regulation cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication cellular process excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling activation of cysteine-type endopeptidase activity regulation of catalytic activity positive regulation of protein metabolic process positive regulation of peptidase activity protein maturation regulation of primary metabolic process positive regulation of molecular function positive regulation of metabolic process regulation of proteolysis proteolysis regulation of endopeptidase activity positive regulation of macromolecule metabolic process protein metabolic process zymogen activation regulation of cysteine-type endopeptidase activity regulation of protein metabolic process regulation of peptidase activity positive regulation of catalytic activity primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of molecular function positive regulation of hydrolase activity biosynthetic process positive regulation of cysteine-type endopeptidase activity regulation of hydrolase activity positive regulation of endopeptidase activity positive regulation of proteolysis protein processing metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process programmed cell death catabolic process protein catabolic process macromolecule catabolic process glutamate receptor signaling pathway behavior learning or memory cognition memory amine metabolic process catecholamine metabolic process phenol-containing compound metabolic process organic hydroxy compound metabolic process dopamine metabolic process catechol-containing compound metabolic process biogenic amine metabolic process protein localization protein localization to postsynaptic membrane protein localization to cell periphery cellular localization protein localization to synapse localization within membrane protein localization to membrane localization cellular macromolecule localization macromolecule localization protein localization to postsynapse protein localization to cell junction startle response neuromuscular process response to external stimulus regulation of neuronal synaptic plasticity regulation of synaptic plasticity response to stress response to wounding monoatomic cation transmembrane transport transmembrane transport transport monoatomic ion transmembrane transport monoatomic ion transport monoatomic cation transport establishment of localization negative regulation of biological process negative regulation of protein catabolic process negative regulation of cellular process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process negative regulation of metabolic process regulation of catabolic process regulation of protein catabolic process neurogenesis cellular developmental process cell differentiation synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic positive regulation of synaptic transmission positive regulation of synaptic transmission, glutamatergic regulation of localization regulation of transport regulation of monoatomic ion transport regulation of monoatomic ion transmembrane transport regulation of transmembrane transport regulation of monoatomic cation transmembrane transport response to light stimulus learning visual learning visual behavior associative learning response to radiation response to abiotic stimulus ammonium ion metabolic process serotonin metabolic process indole-containing compound metabolic process primary amino compound metabolic process response to alcohol response to oxygen-containing compound response to ethanol sleep directional locomotion locomotion calcium ion transmembrane import into cytosol inorganic ion transmembrane transport calcium ion transport metal ion transport inorganic cation transmembrane transport calcium ion transmembrane transport ligand-gated ion channel signaling pathway ionotropic glutamate receptor signaling pathway response to amine response to nitrogen compound response to amphetamine excitatory chemical synaptic transmission sensory perception sensory perception of pain long-term synaptic potentiation	postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic specialization membrane postsynaptic specialization synapse membrane plasma membrane postsynaptic density membrane synaptic membrane cell periphery postsynaptic density postsynapse cellular anatomical structure neuron to neuron synapse organelle cell junction postsynaptic membrane asymmetric synapse plasma membrane region presynapse presynaptic membrane glutamatergic synapse neuron spine neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection dendrite dendritic tree membrane-bounded organelle intracellular anatomical structure transport vesicle intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle synaptic vesicle secretory vesicle cytoplasm vesicle exocytic vesicle protein-containing complex plasma membrane protein complex membrane protein complex transporter complex NMDA selective glutamate receptor complex receptor complex ionotropic glutamate receptor complex neurotransmitter receptor complex transmembrane transporter complex plasma membrane signaling receptor complex monoatomic ion channel complex cell surface organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane cytoplasmic vesicle membrane vesicle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
B	IPR001508	Ionotropic glutamate receptor, metazoa	Family
B	IPR001828	Receptor, ligand binding region	Domain
B	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
B	IPR049873	Glutamate [NMDA] receptor subunit 1-like, N-terminal LIVBP-like domain	Domain
B	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
B	IPR015683	Ionotropic glutamate receptor	Family
B	IPR049872	Glutamate [NMDA] receptor subunit 1-like, ligand-binding domain	Domain
A	IPR018884	Glutamate [NMDA] receptor, epsilon subunit, C-terminal	Domain
A	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
A	IPR001508	Ionotropic glutamate receptor, metazoa	Family
A	IPR001828	Receptor, ligand binding region	Domain
A	IPR001320	Ionotropic glutamate receptor, C-terminal	Domain
A	IPR019594	Ionotropic glutamate receptor, L-glutamate and glycine-binding domain	Domain
A	IPR015683	Ionotropic glutamate receptor	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q05586	intellectual disability, autosomal dominant 8 Pain cocaine dependence intellectual disability trigeminal neuralgia cocaine abuse schizoaffective disorder lung adenocarcinoma neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive atypical teratoid rhabdoid tumor postencephalitic Parkinson disease glioblastoma schizophreniform disorder Sjogren syndrome large cell medulloblastoma intellectual disability, autosomal dominant 8 Pain cocaine dependence intellectual disability trigeminal neuralgia cocaine abuse schizoaffective disorder lung adenocarcinoma neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive atypical teratoid rhabdoid tumor postencephalitic Parkinson disease glioblastoma schizophreniform disorder Sjogren syndrome large cell medulloblastoma malignant ependymoma medulloblastoma oligodendroglioma bipolar disorder Pick disease primitive neuroectodermal tumor subependymal giant cell astrocytoma malignant glioma osteosarcoma astrocytic tumor Parkinson disease pilocytic astrocytoma
A	Pharos: Q12879	Landau-Kleffner syndrome epilepsy rolandic epilepsy melanoma autism colorectal cancer morphine dependence schizophrenia substance withdrawal syndrome bipolar disorder speech disorder Language Development Disorders depressive disorder oligodendroglioma Parkinson disease Landau-Kleffner syndrome epilepsy rolandic epilepsy melanoma autism colorectal cancer morphine dependence schizophrenia substance withdrawal syndrome bipolar disorder speech disorder Language Development Disorders depressive disorder oligodendroglioma Parkinson disease pilocytic astrocytoma psoriasis subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor large cell medulloblastoma lung carcinoma medulloblastoma continuous spikes and waves during sleep opiate dependence postencephalitic Parkinson disease glioblastoma astrocytic tumor auditory perceptual disorders Lennox-Gastaut syndrome autism spectrum disorder malignant ependymoma colorectal carcinoma cutaneous melanoma neurodegenerative disease ovarian cancer Pick disease primitive neuroectodermal tumor hepatitis B virus infection intellectual disability attention deficit hyperactivity disorder, inattentive type toxic encephalopathy malignant glioma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.